The whale shark, Rhincodon typus, is a long-lived migratory species inhabiting tropical and warm-temperate waters worldwide. Seasonal aggregations of whale sharks in shallow coastal waters of many countries have led to the development of ecotourism industries. Whale sharks that aggregate seasonally at Ningaloo Reef in Western Australia have a migration range within Indonesian and Southeast Asian waters. However, very little is known about their behaviour, local migration patterns, or potential threats faced in this region. In this study, we investigated traditional ecological knowledge of whale sharks through interviews with Bajo and other fishers from five settlements in the Timor and Roti Islands in eastern Indonesia. We found that there are culturally driven prohibitions and customary beliefs concerning whale sharks among Bajo fishermen, who commonly sight sharks in the Timor Sea, in southern Indonesian and Timor Leste waters. Sightings are most common during the months of August to December. Interviews also indicate a low level of harvesting of whale sharks in the region. The results demonstrate the potential for combining traditional ecological knowledge and new technology to develop whale shark management strategies, and to determine the predictability of whale shark appearances as one vital factor in assessing the potential for development of small-scale whale shark ecotourism initiatives.